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Port details
ddocent Bash pipeline for RAD sequencing
2.7.8_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.7.8_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-20 01:34:22
Last Update: 2021-09-30 21:23:30
Commit Hash: 620968a
Also Listed In: java perl5 python
License: MIT
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (22 items)
Collapse this list.
  1. /usr/local/share/licenses/dDocent-2.7.8_1/catalog.mk
  2. /usr/local/share/licenses/dDocent-2.7.8_1/LICENSE
  3. /usr/local/share/licenses/dDocent-2.7.8_1/MIT
  4. bin/ErrorCount.sh
  5. bin/RefMapOpt.sh
  6. bin/ReferenceOpt.sh
  7. bin/Rename_SequenceFiles.sh
  8. bin/Rename_for_dDocent.sh
  9. bin/Rename_for_dDocent_with-INDEX.sh
  10. bin/dDocent
  11. bin/dDocent_filters
  12. bin/dDocent_ngs.sh
  13. bin/ddocent-assembly-test
  14. bin/ddocent-assembly-test-cleanup
  15. bin/filter_hwe_by_pop.pl
  16. bin/filter_missing_ind.sh
  17. bin/pop_missing_filter.sh
  18. bin/remake_reference.sh
  19. bin/remove.bad.hap.loci.sh
  20. @owner
  21. @group
  22. @mode
Collapse this list.
Dependency lines:
  • dDocent>0:biology/ddocent
To install the port: cd /usr/ports/biology/ddocent/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/ddocent
  • pkg install dDocent
PKGNAME: dDocent
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
dDocent
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd642.7.8_12.7.8_1
FreeBSD:11:armv6--
FreeBSD:11:i3862.7.8_12.7.8_1
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd642.7.8_12.7.8_1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386-2.7.8_1
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd642.7.8_12.7.8_1
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386-2.7.8_1
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd642.7.8_1-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3862.7.8_1-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. python3.8 : lang/python38
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. mawk>=0 : lang/mawk
  2. gawk>=0 : lang/gawk
  3. coreutils>=0 : sysutils/coreutils
  4. gnuplot>=0 : math/gnuplot
  5. parallel>=0 : sysutils/parallel
  6. bash : shells/bash
  7. bwa>=0.7.13 : biology/bwa
  8. cd-hit>=0 : biology/cd-hit
  9. samtools>=1.3 : biology/samtools
  10. vcftools>=0.1.15 : biology/vcftools
  11. trimmomatic>=0 : biology/trimmomatic
  12. bamtools>=0 : biology/bamtools
  13. stacks>=0 : biology/stacks
  14. rainbow>=0 : biology/rainbow
  15. trimadap>=0 : biology/trimadap
  16. seqtk>=0 : biology/seqtk
  17. bedtools>=2.26.0 : biology/bedtools
  18. pear-merger>=0 : biology/pear-merger
  19. vcflib>=0 : biology/vcflib
  20. freebayes : biology/freebayes
  21. fastp : biology/fastp
  22. java : java/openjdk8
  23. python3.8 : lang/python38
  24. perl5>=5.32.r0<5.33 : lang/perl5.32
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/jpuritz/dDocent/tar.gz/v2.7.8?dummy=/
Collapse this list.

Number of commits found: 7

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
30 Sep 2021 21:23:30
 files touched by this commit commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7  2.7.8_1
rene search for other commits by this committer
cleanup: drop support for EOL FreeBSD 11.X

Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11

Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*

Reviewed by:	doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.7.8_1
mat search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.7.8_1
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  2.7.8_1
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
04 May 2019 15:09:10
Original commit files touched by this commit Revision:500812  2.7.8
jwb search for other commits by this committer
biology/ddocent: Upgrade to 2.7.8

Reported by:    portscout
12 Dec 2018 01:35:36
Original commit files touched by this commit Revision:487272  2.2.25_1
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
20 Apr 2018 01:34:05
Original commit files touched by this commit Revision:467808  2.2.25
jwb search for other commits by this committer
biology/ddocent: Bash pipeline for RAD sequencing

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15139

Number of commits found: 7